On Fri, May 31, 2013 at 9:14 AM, WuChaofu <xiaowu759_at_hotmail.com> wrote:
> Dear VMDers,
> I want to place the origin point at the position of an atom. How to compose a tcl code to realize it? Please give me some hints. Thanks a lot.

you don't need a complicated Tcl script, but just a little thinking an
exactly one command.
this is essentially a trivial exercise in spatial geometry: what is
the translation vector that makes it that the coordinate of your
reference atom become {0 0 0}? the rest of the answer you'll find the
VMD User's Guide.